Population structure of Puccinia striiformis f. sp. tritici, the cause of wheat stripe rust, in western Canada

Stripe rust of wheat, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most devastating diseases of wheat worldwide. Selection pressure on the pathogen population may result in a rapid shift to races virulent on wheat genotypes with specific resistance genes. For successful stripe rust management, it is important to monitor the virulence spectrum of the pathogen to detect new races. The purpose of this research was to survey Saskatchewan fields to determine the prevalence of stripe rust, characterize the race structure of Pst in western Canada and to determine the genotypic diversity of the pathogen population. Race characterization was performed by inoculating 27 near-isogenic wheat lines carrying 28 known resistance genes, four supplemental cultivars and one triticale cultivar with 61 genetically uniform Pst isolates from western Canada. Whole genome sequencing of pathogen isolates was conducted, using the Illumina HiSeq2500 platform and polymorphisms were assessed by single nucleotide polymorphism (SNP) variants. Characterization of Pst isolates identified 33 races of the pathogen. Genes Yr5, Yr15 and YrSP conditioned resistance against all isolates tested and all isolates were virulent on Yr6, Yr7, Yr9, Yr18, Yr28, Yr29 and Yr31. Variation for virulence was observed among isolates on Yr10, Yr24, YrTye, YrSu, Yr3 and Yr4. The analyses of virulence profiles divided the 61 isolates into four sub-populations or groups. These four sub-populations were distinct from each other in terms of virulence spectrum and year of collection. The Pst population in Alberta had greater diversity in terms of virulence compared with the Saskatchewan population. Diversity at the genome level was not observed to be related to geographic location or virulence phenotypes of the isolates. The SNP data revealed four sub-populations in the western Canadian Pst population. Genomic analyses of 48 Pst isolates did not reveal any relationship of the four sub-populations with their origin or year of collection. Signs of recombination were detected in the Pst population in western Canada. Genomic analyses differentiated isolates showing signs of recombination from those that did not